Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Vertical changes in water depth and environmental variables drove the antibiotics and antibiotic resistomes distribution, and microbial food web structures in the estuary and marine ecosystems

The influence of vertical changes in water depth on emerging pollutants distribution and microbial food web remains elusive. We investigated the influence of vertical transition in water depth on the environmental variables, antibiotics and antibiotic resistomes, and microbial community structures in estuary and marine ecosystems (0-50 m). Stepwise multiple linear regression model showed that among investigated environmental variables, change in water salinity was the most influential factor dictating the fluoroquinolone and macrolides concentrations, while dissolved oxygen and turbidity were the key influencers of sulfonamides and beta-lactam concentrations, respectively. Bacterial and eukaryotic diversity and niche breadth significantly increased with the increasing water depth. Ecosystem food web structure at the bottom depths was more stable than at the middle and surface depths. At the surface depth, the top 5 keystone genera were Cryothecomonas, Syndiniales, Achromobacter, Pseudopirsonia, and Karlodinium. Whereas Eugregarinorida, Neptuniibacter, Mychonastes, Novel_Apicomplexa_Class_1, Aplanochytrium and Dietzia, Halodaphnea, Luminiphilus, Aplanochytrium, Maullinia dominated the top 5 genera at the middle and the bottom depth, respectively. Absolute abundance of antibiotic resistance genes (ARGs) was drastically increased at the surface depth compared with the middle and bottom depths. Abundance of the top 10 ARGs and mobile genetic elements (MGEs) detected including tnpA-05, aadA2-03, mexF, aadA1, intI-1(clinic), qacEdelta1-02, aadA-02, qacEdelta1-01, cmlA1-01, and aadA-01 were amplified at the surface depth. This study demonstrated that ARGs abundance was disproportionate to bacterial diversity, and anthropogenic disturbances, confinement, MGEs, and ecosystem stability play primary roles in the fate of ARGs. The findings of this study also implicate that vertical changes in the water depth on environmental conditions can influence antibiotic concentrations and microbial community dramatically.

Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China

AIM

This study aimed to investigate the high-resolution phenotypic and genotypic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli strains isolated from hospitalized patients to explore the resistance genes and mobile genetic elements (MGEs) involved in horizontal dissemination.

METHODS

Between May and September 2021, a total of 216 ESBL-producing E. coli isolates were recovered from multiple departments. The identification of strains was performed using MALDI-TOF mass spectrometry and PCR, while antibiotic susceptibility testing was carried out using the Vitek 2 COMPACT system to determine resistance patterns, while PCR was used to detect different resistance genes and MGEs. In addition, a conjugation assay was performed to investigate the horizontal gene transfer of resistance genes. Selected isolates underwent whole-genome sequencing using the Illumina MiSeq platform.

RESULTS

A total of 216 out of 409 E. coli isolates recovered from a tertiary hospital were observed to be ESBL-producing, giving a carriage rate of 52.8%, as determined by phenotypic screening. The most frequent sources of ESBL-producing E. coli isolates were urine (129/216, 59.72%,) and blood (50/216, 23.14%). The most prevalent ESBL genes identified were blaCTX-M (60.18%), blaTEM (40.27%), and blaSHV (18.05%). Three E. coli isolates were found to carry the genes blaNDM, mcr-1, and fosA3 genes. The most prevalent MGEs were IS26 (95.37%), Int (87.03%), and IncFIB (76.85%). Whole-genome sequencing analysis of eight MDR E. coli strains revealed that these isolates belonged to eight different sequence types (STs) and serotypes and were found to harbor multiple plasmid replicons and virulence factors.

CONCLUSION

This study highlights a high incidence of antibiotic resistance genes and MGEs associated with the dissemination of ESBLs and other resistance genes.

Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage

Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.

Escherichia coli inhibits endometriosis by inducing M1 polarity of peritoneal macrophages and the IL-1 signaling pathway

The development of endometriosis is closely linked to macrophages, and the type M1 macrophage has been hypothesized to play an inhibitory role in its progression. Escherichia coli induces macrophage polarization toward M1 in numerous diseases and differs in the reproductive tract of patients with and without endometriosis; however, its specific role in endometriosis development remains unknown. Therefore, in this study, E. coli was selected as a stimulator to induce macrophages, and its effects on the growth of endometriosis lesions in vitro and in vivo were investigated using C57BL/6N female mice and endometrial cells. It was revealed that E. coli inhibited the migration and proliferation of co-cultured endometrial cells by IL-1 in vitro and prevented the growth of lesions and induced macrophage polarization toward M1 in vivo. However, this change was counteracted by C-C motif chemokine receptor 2 inhibitors, suggesting that it was associated with bone marrow-derived macrophages. Overall, the presence of E. coli in the abdominal cavity may be a protective factor for endometriosis.

Occurrence of multiple bisphenol S analogues in children from Shantou, China

Emerging bisphenol S analogues (BPSs) have gained their application perspectives to replace bisphenol A (BPA) and BPA analogues (BPAs). However, the extent of human exposure and potential health risk from BPSs is rarely known yet. We hypothesized that children living in Shantou, China, a well-known e-waste recycling city, may expose to emerging BPSs together with BPA and BPAs. In this study, BPA, six commonly used BPAs and 11 emerging BPSs were determined simultaneously in 240 urine samples collected from children residing in Shantou. BPA, BPS, bisphenol F, bisphenol AF and three BPSs of 2,4'-bis(hydroxyphenyl)sulfone, 4-((4-(allyloxy)phenyl)sulfonyl)phenol and diphenylsulfone (DPS) were the urinary predominant bisphenols with detection frequencies of 67-100% in the children. BPA was found at the highest median concentration (3.36 µg/g creatinine) followed by BPS (0.313) and DPS (0.187). It is interesting to find that the girls and children in the younger group (2 ≤ age < 5) had consistently higher concentrations of the seven dominant bisphenols than the boys and these of the older group (5 ≤ age ≤ 10), respectively. The children with under/overweight suffered higher burdens of bisphenol exposure based on medians of estimated daily intakes. Association analysis results indicated that the Shantou children exposed themselves to multiple BPSs along with BPA and BPAs from assumed consumer products and/or contaminated environments.

Occurrence of emerging bisphenol S analogues in urine from five occupational populations in South China

Bisphenol S (BPS) and its 11 emerging analogues were investigated in 325 urine samples from five occupational populations in South China. Besides BPS, ten emerging BPS analogues were newly identified and detected in the urine. It should be noted that urinary concentrations of dominant BPS analogues of 2,4'-bis(hydroxyphenyl)sulfone (2,4-BPS), bis(3-allyl-4-hydroxyphenyl)sulfone (TGSA) and diphenylsulfone (DPS) were 1.1-2.3 times higher than that of BPS, with overall detection frequencies at 74-91 %. The median sum concentrations of the target 12 bisphenols (ng/mL) were found highest in urine from cashiers (1.12), followed by water plant staffs (0.994), teachers (0.552), doctors (0.408) and power plant staffs (0.333). The composition profile of the urinary dominant bisphenols was occupational-dependent, with 2,4-BPS accounting for 45-73 % in cashiers and power plant staffs, and with DPS and TGSA for 74-82 % among doctors, teachers and water plant staffs. Significant correlations were found among the most frequently detected bisphenols in cashiers, indicating their common application and emission pathways. The median exposures based on estimated daily intakes (EDIs, ng/kg bw/day) for the 12 bisphenols in cashiers and water plant staffs (31.6-35.6) were 1.8-3.4 times higher than those of teachers, doctors and power plant staffs (10.6-17.5). This is the first study to identify multiple emerging BPS analogues in urine from occupational populations, especially cashiers and water plant staffs.

Loss of erm(B)-Mediated rRNA Dimethylation and Restoration of Erythromycin Susceptibility in Erythromycin-Resistant Enterococci Following Induced Linezolid Resistance

Linezolid has been reported to restore erythromycin susceptibility in erythromycin-resistant Staphylococcus aureus. This phenomenon has not been reported in enterococci and the mechanisms involved therein are still unknown. The purpose of this study was to investigate the mechanisms involved and the effect of combining linezolid with erythromycin on erythromycin-resistant enterococci. Checkerboard techniques were used to determine drug interactions, and 12 of 14 isolates showed a synergistic effect between erythromycin and linezolid (fractional inhibitory concentration <0.5). We observed that the erm(B) gene, which encodes a dimethyltransferase responsible for erythromycin resistance, was expressed from transposon Tn1545 in the tested erythromycin-resistant enterococci. After exposure to linezolid, erm(B)-mediated rRNA dimethylation at A2071 could not be detected, and the erm(B) gene was lost following acquisition of erythromycin susceptibility. Thus, in conclusion, linezolid combined with erythromycin exerts a synergistic effect against erythromycin-resistant enterococci. Linezolid treatment suppressed erm(B)-mediated rRNA dimethylation at A2071, which could lead to loss of the erm(B) gene.

Roles of vaginal flora in human papillomavirus infection, virus persistence and clearance

Vaginal flora plays a vital role in human papillomavirus (HPV) infection and progression to cancer. To reveal a role of the vaginal flora in HPV persistence and clearance, 90 patients with HPV infection and 45 healthy individuals were enrolled in this study and their vaginal flora were analyzed. Women with HPV infection were treated with Lactobacillus in the vaginal environment as a supplement to interferon therapy. Our results indicated that patients with high risk HPV (Hr-HPV) 16/18 infection had a significantly higher alpha diversity compared with the healthy control (p < 0.01), while there was no significant difference between the non-Hr-HPV16/18 group and the controls (p > 0.05). Patients with multiple HPV infection had insignificantly higher alpha diversity compared with single HPV infection (p > 0.05). The vaginal flora of patients with HPV infection exhibited different compositions when compared to the healthy controls. The dominant bacteria with the highest prevalence in HPV-positive group were Lactobacillus iners (n = 49, 54.44%), and the top 3 dominant bacteria in the HPV-persistent group were Lactobacillus iners (n = 34, 53.13%), Sneathia amnii (n = 9, 14.06%), and Lactobacillus delbrueckii (n = 3, 4.69%). Patients with HPV clearance had significantly lower alpha diversity, and the flora pattern was also different between groups displaying HPV clearance vs. persistence. The patients with persistent HPV infection had significantly higher levels of Bacteroidaceae, Erysipelotrichaceae, Helicobacteraceae, Neisseriaceae, Streptococcaceae (family level), and Fusobacterium, Bacteroides, Neisseria, and Helicobacter (genus level) than patients who had cleared HPV (p < 0.05).

Importance

Our study revealed differences in vaginal flora patterns are associated with HPV persistence and its clearance. Interferon plus probiotics can greatly improve virus clearance in some patients. Distinguishing bacterial features associated with HPV clearance in patients would be helpful for early intervention and reverse persistent infection.

Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.

Ecological mechanisms of sedimental microbial biodiversity shift and the role of antimicrobial resistance genes in modulating microbial turnover

The mechanisms of phylogenetic turnover of microbial communities to environmental perturbations in sediments remain unclear. In this study, the molecular mechanisms of phylogenetic turnover, and impact of antibiotics and antibiotic resistance genes (ARGs) on the modification of microbial assemblages were unravelled. We investigated 306 ARGs, 8 transposases, and 4 integron integrases, bacteria, and eukaryotic diversity through high-throughput quantitative PCR and illumina sequencing, 21 antibiotics and 3 tetracycline byproducts. The freshwater and estuary ecosystems were mainly dominated by genus Sulfurovum and colonised by closely related species compared with the estuary (closeness centrality = 0.42 vs. 0.46), which was dominated by genus Mycobacterium. Eighty-six percent of the ecological process in the bacterial community was driven by stochastic processes, while the rest was driven by deterministic processes. Environmental-related concentrations of antibiotics (0.15-32.53 ng/g) stimulated the proliferation of ARGs which potentially modulated the microbial community assembly. ARG acquisition significantly (P < 0.001) increased eukaryotic diversity through protection mechanisms. ARGs showed complex interrelationships with the microbial communities, and phylum arthropods and Nematea demonstrated the strongest ARG acquisition potential. This study provides key insights for environmental policymakers into understanding the ecological impact of antibiotics and the role of ARGs in modulating the phylogenetic turnover of microbial communities and trophic transfer mechanisms.

Photodynamic therapy treats acne by altering the composition of the skin microbiota

BACKGROUND

Acne is the eighth-most prevalent inflammatory skin disease with no optimal treatment. Photodynamic therapy (PDT) is an effective treatment for severe acne.

AIMS

The effect of PDT on the composition and diversity of skin microflora in severe acne patients was studied.

MATERIALS AND METHODS

A total of 18 patients with severe acne and 8 healthy individuals were selected for this study. Patients were treated with 5-aminolevulinic acid-mediated PDT once a week three times in total; the skin microbiome was measured by 16S ribosomal RNA gene sequencing before and after treatment (1 week after each PDT).

RESULTS

The microflora composition was different between healthy controls and patients, and between patients before and after treatment. Alpha diversity indices were lower in patients than those in control. There were 15 bacterial genera with high relative abundance that had noticeable changes during treatment. At the genus level,particularly Cutibacterium acnes (C. acnes formerly Propionibacterium acnes), there was no statistically significant difference among different group. The abundances of Staphylococcus epidermidis and Staphylococcus aureus were low.

DISCUSSION

The microbial composition is different between severe acne patients acne patients and healthy individuals. The therapeutic efficacy of severe acne treated with PDT is associated with the composition and diversity of skin microbiota.

CONCLUSION

The skin microbial composition changes after PDT treatment. PDT is an effective method for the treatment of severe acne.

Machine Learning Techniques for Antimicrobial Resistance Prediction of Pseudomonas Aeruginosa from Whole Genome Sequence Data

AIM

Due to the growing availability of genomic datasets, machine learning models have shown impressive diagnostic potential in identifying emerging and reemerging pathogens. This study aims to use machine learning techniques to develop and compare a model for predicting bacterial resistance to a panel of 12 classes of antibiotics using whole genome sequence (WGS) data of Pseudomonas aeruginosa.

METHOD

A machine learning technique called Random Forest (RF) and BioWeka was used for classification accuracy assessment and logistic regression (LR) for statistical analysis.

RESULTS

Our results show 44.66% of isolates were resistant to twelve antimicrobial agents and 55.33% were sensitive. The mean classification accuracy was obtained ≥98% for BioWeka and ≥96 for RF on these families of antimicrobials. Where ampicillin was 99.31% and 94.00%, amoxicillin was 99.02% and 95.21%, meropenem was 98.27% and 96.63%, cefepime was 99.73% and 98.34%, fosfomycin was 96.44% and 99.23%, ceftazidime was 98.63% and 94.31%, chloramphenicol was 98.71% and 96.00%, erythromycin was 95.76% and 97.63%, tetracycline was 99.27% and 98.25%, gentamycin was 98.00% and 97.30%, butirosin was 99.57% and 98.03%, and ciprofloxacin was 96.17% and 98.97% with 10-fold-cross validation. In addition, out of twelve, eight drugs have found no false-positive and false-negative bacterial strains.

CONCLUSION

The ability to accurately detect antibiotic resistance could help clinicians make educated decisions about empiric therapy based on the local antibiotic resistance pattern. Moreover, infection prevention may have major consequences if such prescribing practices become widespread for human health.

New insight into the microbiome, resistome, and mobilome on the dental waste water in the context of heavy metal environment

Object

Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW.

Methods

DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods.

Results

DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs.

Conclusion

DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.

Coexistence of bla NDM-5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China

The emergence of pathogens is conferring resistance to last-resort therapies such as tigecycline, colistin, and carbapenems, limiting the therapeutic options, and raising concerns about the emergence of new "superbugs." This study reports the first incident of a bla _NDM-5 and tet(X4) co-harboring Escherichia coli with resistance to carbapenem and tigecycline recovered as the causative agent of a urinary tract infection in a 94-year-old patient. The E. coli strain ECCL209 carries multiple resistance genes [i.e., bla _TEM-1B , bla _NDM-5, bla _CMY-2, aadA22, florR, erm(B), mph(A), erm(42), lnuG, qnrS1, and sul2] and exhibits resistance to almost all clinically used antibiotics. MLST analysis found that the strain belongs to ST648, considered a worldwide high-risk pandemic clone. Moreover, multiple plasmid incompatibility types were detected, i.e., IncHI1A, IncHI1B, IncFII, IncFIA, IncFIB, IncQ1, Col, and IncX4. Genetic analysis revealed that bla _NDM-5 and tet(X4) genes were localized on two hybrid plasmids with multiple replicons. Continuous monitoring studies are suggested to quantify the antimicrobial resistance and assess the dissemination of such superbugs into a human healthcare setting.

Synergistic Activity of Tetrandrine and Colistin against mcr-1-Harboring Escherichia coli

Before the emergence of plasmid-mediated colistin resistance, colistin was once considered the last drug of choice for infections caused by carbapenem-resistant bacteria. Currently, researchers are relentlessly exploring possible alternative therapies that could efficiently curb the spread of drug resistance. In this study, we aim to investigate the synergistic antibacterial activity of tetrandrine in combination with colistin against mcr-1-harboring Escherichia coli. We examined the antibacterial activity of tetrandrine in combination with colistin in vivo and in vitro and examined the bacterial cells by fluorescence, scanning, and transmission electron microscopy (TEM) to explore their underlying mechanism of action. We further performed a computational analysis of MCR-1 protein and tetrandrine to determine the interaction interface of these two molecules. We confirmed that neither colistin nor tetrandrine could, on their own, inhibit the growth of mcr-1-positive E. coli. However, in combination, tetrandrine synergistically enhanced colistin activity to inhibit the growth of E. coli both in vivo and in vitro. Similarly, molecular docking showed that tetrandrine interacted with the three crucial amino acids of the MCR-1 protein in the active site, which might inhibit MCR-1 from binding to its substrates, cause MCR-1 to lose its ability to confer resistance. This study confirmed that tetrandrine and colistin have the ability to synergistically overcome the issue of colistin resistance in mcr-1-harboring E. coli.

Incidence and molecular characterization of ESBL-producing and colistin-resistant Escherichia coli isolates recovered from healthy food-producing animals in Pakistan

OBJECTIVES

To investigate the occurrence and molecular features of ESBL-producing and colistin-resistant Escherichia coli isolates recovered from healthy food-producing animals in Pakistan.

METHODS

A total of 153 E. coli isolates were recovered from 250 faecal samples collected from livestock and poultry. The antibiotic susceptibility, resistant determinants and mobile genetic elements were determined for all the isolates. The clonal relatedness was analysed by MLST. Plasmids harbouring, localization and transferability of mcr-1 gene were carried out by Southern hybridization, S1-PFGE and transconjugation.

RESULTS

Out of 153 E. coli strains, 49.01% isolates were ESBLs producers, whereas 18.95% were resistant to colistin and 84.31% of the isolates. Multidrug resistance was found in 84% of the isolates. The ESBL-producing E. coli in buffaloes, cattle, sheep, goat and broilers faecal samples were 60%, 74%, 54%, 50% and 68%, respectively. Among the ESBLs genes, bla_CTX-M was the most prevalent group detected in 98.66%, while only mcr-1 of the colistin-resistant genes could be PCR amplified in 29 isolates. The common MGEs found were ISECP1 (35.13%), ISCR1 (33.78%), ISApl1 (20.27%) and Inti1 (58.10%). The most predominant Inc. types found were IncFIB 46.66%, followed by IncFIA 30.66%, IncFIC 26.66%, IncFrepB 26.66%, IncHI2 26.66%, IncP 22.66% and IncX4 21.33%. The most frequent sequence type detected was ST58. Southern blot and S1-PFGE confirmed the plasmid harbouring of mcr-1 gene.

CONCLUSION

The co-occurrence of mcr-1 and ESBLs-encoding genes, along with MGEs in E. coli from healthy food animals in Pakistan, is a major concern.

SIGNIFICANCE AND IMPACT OF STUDY

Antimicrobial resistance can be transferred from animals to humans by direct contact or via the food chain and environment. The prevalence and co-occurrence of ESBL and colistin resistance genes from food-producing animals is rare in Pakistan. To our knowledge, this is the first report to find ESBLs and mcr-1-harbouring E. coli from the faecal samples of the healthy food-producing animals in Pakistan. The presence of ARGs in association with MGEs, co-harbouring the virulence factors, as determined in the current study, is a severe threat to livestock and the human community as it has horizontally and food web transferability.

A unique Levey-Jennings control chart used for internal quality control in human papillomavirus detection

OBJECTIVE

The purpose of this study was to provide an updated estimate of the prevalences of different types of human papillomavirus (HPV) in females in Chaoshan District and to establish an internal quality control (IQC) method for excluding false-positive results in HPV detection by using the Levey-Jennings control chart.

METHOD

HPV types were detected in 23,762 cervical samples by using PCR membrane hybridization. The means and standard deviations (SDs) of the positive rates were calculated, the Levey-Jennings chart was plotted, and the rules for "out of control" and "warning" were established. A set of standardized IQC for HPV DNA tests was developed based on the values and Levey-Jennings charts.

RESULT

In 466 batches, the positive rate exceeded the 1 + 2SD rule 24 times, but there was no consecutive exceedance, which was considered "in control". When the positive rate exceeded the 1 + 3SD rule 8 times with consecutive exceedance, it was considered "out of control". Further examination revealed that detections showing "out of control" had an undesirable random error, indicating that contamination may occur due to improper operation.

CONCLUSION

This unique Levey-Jennings control chart is a practical method for eliminating false-positive results in HPV DNA detection and should be widely applicable in molecular diagnostic laboratories.

Surveillance of SARS-CoV-2 antibodies of patients in the local affected area during Wuhan lockdown

BACKGROUND

Serosurveillance is crucial in estimating the range of SARS-CoV-2 infections, predicting the possibility of another wave, and deciding on a vaccination strategy. To understand the herd immunity after the COVID-19 pandemic, the seroprevalence was measured in 3062 individuals with or without COVID-19 from the clinic.

METHODS

The levels of SARS-CoV-2 antibody IgM and IgG were measured by the immuno-colloidal gold method. A fusion fragment of nucleocapsid and spike protein was detected by a qualitative test kit with sensitivity (89%) and specificity (98%).

RESULTS

The seroprevalence rate for IgM and IgG in all outpatients was 2.81% and 7.51%, respectively. The sex-related prevalence rate of IgG was significantly higher (P < 0.05) in women than men. The highest positive rate of IgM was observed in individuals < 20 years of age (3.57%), while the highest seroprevalence for IgG was observed in persons > 60 years of age (8.61%). Positive rates of IgM and IgG in the convalescent patients were 31.82% and 77.27%, respectively, which was significantly higher than individuals with suspected syndromes or individuals without any clinical signs (P < 0.01). Seroprevalence for IgG in medical staff was markedly higher than those in residents. No significant difference of seroprevalence was found among patients with different comorbidities (P > 0.05).

CONCLUSIONS

The low positive rate of the SARS-CoV-2 IgM and nucleic acid (NA) test indicated that the SARS-CoV-2 outbreak is subsiding after 3 months, and the possibility of reintroduction of the virus from an unidentified natural reservoir is low. Seroprevalence provides information for humoral immunity and vaccine in the future.

Clinical Significance of Fusobacterium nucleatum and Microsatellite Instability in Evaluating Colorectal Cancer Prognosis

OBJECTIVE

Both genetic and microbial factors play important roles in colorectal cancer (CRC) development. The effects of Fusobacterium nucleatum (F. nucleatum) and microsatellite instability (MSI) on CRC prognosis require more clinical evidence. We aimed to investigate the role of F. nucleatum and MSI as biomarkers in predicting the prognosis of CRC.

METHODS

CRC patients in various TNM stages were enrolled. MSI status and F. nucleatum were detected by immunohistochemical staining of formalin-fixed paraffin-embedded (FFPE) specimens. The associations between MSI status and F. nucleatum and clinical parameters were analyzed.

RESULTS

MSI tumors were more frequently observed in the colon than in the rectum. Cancerous tissues had higher levels of F. nucleatum than adjacent noncancerous tissues. There were no significant differences in F. nucleatum abundance in different age, sex, tumor stage, location, and tumor marker groups. MSI status was associated with tumor location and stage. Survival analyses revealed that disease-free survival (DFS) was significantly longer in the F. nucleatum-negative, younger age, and TNM stage I-II groups (p< 0.05), and age, advanced TNM stage (III and IV), and F. nucleatum status were independent factors for poor prognosis. Multivariate Cox regression and receiver operating characteristic (ROC) curve analyses showed that conventional tumor biomarkers of CRC had more prognostic value than F. nucleatum and MSI.

CONCLUSION

Age, advanced TNM stage, and F. nucleatum positivity were independent factors of poor prognosis, suggesting that F. nucleatum and MSI may contribute to the identification of new strategies for the prevention and treatment of CRC.

Genomic diversity of resistant and virulent factors of Burkholderia pseudomallei clinical strains recovered from Guangdong using whole genome sequencing

BACKGROUND

Burkholderia pseudomallei (B. pseudomallei) is a highly infectious agent and causes melioidosis, in both humans and animals, which is endemic in Southeast Asia and Northern Australia.

OBJECTIVES

This study aims to determine the molecular epidemiology, resistant determinants, and genomic diversity of the clinical isolates of B. pseudomallei to further elucidate the phylogenetic and evolutionary relationship of the strains with those in other endemic regions.

METHODS

In this study, we obtained eight clinical B. pseudomallei isolates from Guangdong province from 2018 to 2019. All the isolates were sequenced using the Illumina NovaSeq platform. The draft genomes of B. pseudomallei were further used to find antibiotic-resistant genes (ARGs), virulence factors, and gene mutations. Multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis were performed to characterize the diversity and epidemiology of the strains.

RESULTS

All isolates were susceptible to antibiotics commonly used for melioidosis treatment. Class D beta-lactamases genes OXA-57 and OXA-59, as well as various mutation factors such as amrA, amrB, omp38, gyrA, and ceoB were identified. MLST analysis of the B. pseudomallei strains identified eight different sequence types (STs): ST1774, ST1775, ST271, ST562, ST46, ST830, ST1325, and ST10. Phylogenetic analysis found that the strains used in this study showed high genetic diversity. We also report 165 virulence factors among B. pseudomallei strains responsible for different neurological disorders, pneumonia, skin lesions, and abscesses. All strains recovered in this study were susceptible to commonly used antibiotics. However, high genetic diversity exists among the isolates. The surveillance, diagnosis, and clinical features of melioidosis varied in different geographical locations. These regional differences in the clinical manifestations have implications for the practical management of the disease.

CONCLUSION

The present study reports the identification of different mutation and virulence factors among B. pseudomallei strains responsible for different neurological disorders, pneumonia, skin lesions, and abscesses.

Antimicrobial resistance bacteria and genes detected in hospital sewage provide valuable information in predicting clinical antimicrobial resistance

Extensive use of antibiotics is significantly associated with development of antibiotic-resistant (AR) bacteria. However, their causal relationships have not been adequately investigated, especially in human population and hospitals. Our aims were to understand clinical AR through revealing co-occurrence patterns between antibiotic-resistant bacteria and genes (ARB and ARGs), and their association with antibiotic use, and to consider impact of ARB and ARGs on environmental and human health. Antibiotic usage was calculated based on the actual consumption in our target hospital. ARB was identified by culture. In isolates collected from hospital sewage, bacterial-specific DNA sequences and ARGs were determined using metagenomics. Our data revealed that the use of culture-based single-indicator-strain approaches only captured ARB in 16.17% of the infectious samples. On the other hand, 1573 bacterial species and 885 types of ARGs were detected in the sewage. Furthermore, hospital use of antibiotics influenced the resistance profiles, but the strength varied among bacteria. From our metagenomics analyses, ARGs for aminoglycosides were the most common, followed by sulfonamide, tetracycline, phenicol, macrolides, and quinolones, comprising 82.6% of all ARGs. Association analyses indicated that 519 pairs of ARGs were significantly correlated with ARB species (r > 0.8). The co-occurrence patterns of bacteria-ARGs mirrored the AR in the clinic. In conclusion, our systematic investigation further emphasized that antibiotic usage in hospital significantly influenced the abundance and types of ARB and ARGs in dose- and time-dependent manners which, in turn, mirrored clinical AR. In addition, our data provide novel information on development of certain ARB with multiple antibiotic resistance. These ARB and ARGs from sewage can also be disseminated into the environment and communities to create health problems. Therefore, it would be helpful to use such data to develop improved predictive risk model of AR, to enhance effective use of antibiotics, and to reduce environmental pollution.

Ecological impact of antibiotics on bioremediation performance of constructed wetlands: Microbial and plant dynamics, and potential antibiotic resistance genes hotspots

Constructed wetlands (CWs) are nature-based solutions for treating domestic and livestock wastewater which may contain residual antibiotics concentration. Antibiotics may exert selection pressure on wetland's microbes, thereby increasing the global antibiotics resistance problems. This review critically examined the chemodynamics of antibiotics and antibiotics resistance genes (ARGs) in CWs. Antibiotics affected the biogeochemical cycling function of microbial communities in CWs and directly disrupted the removal efficiency of total nitrogen, total phosphorus, and chemical oxygen demand by 22%, 9.3%, and 24%, respectively. Since changes in microbial function and structure are linked to the emergence and propagation of antibiotic resistance, antibiotics could adversely affect microbial diversity in CWs. The cyanobacteria community seemed to be particularly vulnerable, while Proteobacteria could resist and persist in antibiotics contaminated wetlands. Antibiotics triggered excitation responses in plants and increased the root activities and exudates. Microbes, plants, and substrates play crucial roles in antibiotic removal. High removal efficiency was exhibited for triclosan (100%) > enrofloxacin (99.8%) > metronidazole (99%) > tetracycline (98.8%) > chlortetracycline (98.4%) > levofloxacin (96.69%) > sulfamethoxazole (91.9%) by the CWs. This review showed that CWs exhibited high antibiotics removal capacity, but the absolute abundance of ARGs increased, suggesting CWs are potential hotspots for ARGs. Future research should focus on specific bacterial response and impact on microbial interactions.

Neutrophil-lymphocyte ratio and hypersensitive C-reaction protein are associated with miscarriage during the second trimester of pregnancy

This study investigated whether biomarkers in the second trimester of pregnancy, including the white blood cell (WBC) count, neutrophil-lymphocyte ratio (NLR), hypersensitive C-reactive protein (hs-CRP) concentration, and procalcitonin (PCT) concentration, were associated with miscarriage during the second trimester of pregnancy. Sixty-two asymptomatic patients in their second trimester of pregnancy were included in the control group (group A). Among 67 patients diagnosed with late threatened miscarriage, 46 patients with ongoing pregnancy were included in group B and 21 patients with subsequent miscarriage were included in group C. The serum of these patients was collected and the biomarkers were analyzed. A paired-samples t-test was used for the comparison between the groups before and after the miscarriage. Statistical significance was set at p<0.05. Receiver operating characteristic curve (ROC) analysis was performed to evaluate the predictive value of different biomarkers for miscarriage during the second trimester of pregnancy. WBC count, neutrophil percentage, and hs-CRP levels were significantly higher in group C than in groups A and B (p<0.05). Lymphocyte percentage and albumin levels decreased significantly from group A to group C (p<0.05). In contrast, NLR increased significantly from group A to group C (p<0.05). There was a significant decrease in the WBC count, neutrophil percentage, hemoglobin concentration, and post-miscarriage NLR among the cases with miscarriage (p<0.05). The area under the curve of WBC count, NLR, hs-CRP, and the combination of these three factors for the prediction of late miscarriage varied from 78.0% to 82.6%. The combination of these three factors had the highest specificity of 91.1%, while hs-CRP had the highest sensitivity of 88.9%. WBC count, NLR, and hs-CRP levels are strongly associated with miscarriage during the second trimester of pregnancy, indicating that they are potential predictive biomarkers.

Aberrant cytokine expression in COVID-19 patients: Associations between cytokines and disease severity

Cytokines play pleiotropic, antagonistic, and collaborative in viral disease. The high morbidity and mortality of coronavirus disease 2019 (COVID-19) make it a significant threat to global public health. Elucidating its pathogenesis is essential to finding effective therapy. A retrospective study was conducted on 71 patients hospitalized with COVID-19. Data on cytokines, T lymphocytes, and other clinical and laboratory characteristics were collected from patients with variable disease severity. The effects of cytokines on the overall survival (OS) and event-free survival (EFS) of patients were analyzed. The critically severe and severe patients had higher infection indexes and significant multiple organ function abnormalities than the mild patients (P < 0.05). IL-6 and IL-10 were significantly higher in the critically severe patients than in the severe and mild patients (P < 0.05). IL-6 and IL-10 were closely associated with white blood cells, neutrophils, T lymphocyte subsets, D-D dimer, blood urea nitrogen, complement C1q, procalcitonin C-reactive protein. Moreover, the IL-6 and IL-10 levels were closely correlated to dyspnea and dizziness (P < 0.05). The patients with higher IL-10 levels had shorter OS than the group with lower levels (P < 0.05). The older patients with higher levels of single IL-6 or IL-10 tended to have shorter EFS (P < 0.05), while the patients who had more elevated IL-6 and IL-10 had shorter OS (P < 0.05). The Cox proportional hazard model revealed that IL-6 was the independent factor affecting EFS. IL-6 and IL-10 play crucial roles in COVID-19 prognosis.

Food intake and its effect on the species and abundance of intestinal flora in colorectal cancer and healthy individuals

BACKGROUND/AIM

It is known that an imbalance in the intestinal f lora plays a crucial role in colorectal cancer (CRC), but the effect of food consumption patterns on the types of intestinal flora remains to be clarified. We aimed to analyze the associations between food intake and intestinal flora in healthy and CRC individuals.

METHODS

Food intake data were recorded using the Food Frequency Questionnaire (FFQ). The composition and diversity of the intestinal flora detected by 16S rRNA gene sequencing, and the data were analyzed by R version 3.1.1 software.

RESULTS

Higher intake of red meat or pickled foods, and lower intake of white meat, fruits, vegetables, beans, nuts were found in the CRC group compared with the healthy group. Higher levels of Fusobacteria and Proteobacteria, and lower levels of Firmicutes were observed in the CRC group. Partial correlation analysis revealed that the intake of fruits, beans, and nuts was negatively correlated with Proteobacteria and Fusobacteria, but pickled food was positively correlated with Fusobacteria (p < 0.05). Fish, beans, and nuts intake was negatively correlated with Escherichia (p = 0.01). Multiple regression analysis revealed that vegetable oil (odds ratio [OR], 0.26; 95% confidence interval [CI], 0.13 to 0.82), vegetables (OR, 0.26; 95% CI, 0.10 to 0.64), eggs (OR, 0.26; 95% CI, 0.10 to 0.69), pickled foods (OR, 21.02; 95% CI, 6.02 to 73.45), and red meat (OR, 4.23; 95% CI, 1.68 to 10.60) had an impact on CRC risk.

CONCLUSION

The species and abundance of intestinal flora varies between CRC and healthy individuals and may be affected by their food preference.

Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer

Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF). Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software. Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue. Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method.

A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer

BACKGROUND

Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers.

METHODS

A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies.

RESULTS

Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71.

CONCLUSION

MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.

The Role of Fecal Fusobacterium nucleatum and pks+ Escherichia coli as Early Diagnostic Markers of Colorectal Cancer

BACKGROUND

Accurate analysis of intestinal microbiota will facilitate establishment of an evaluating system for assessing colorectal cancer (CRC) risk and prognosis. This study evaluates the potential role of Fusobacterium nucleatum (F. nucleatum) and Escherichia coli with a pks gene (pks⁺ E. coli) in early CRC diagnosis.

METHODS

We recruited 139 patients, including CRC (n = 60), colorectal adenomatous polyposis (CAP) (n = 37), and healthy individuals (n = 42) based on their colonoscopy examinations. We collected stool and serum samples from the participants and measured the relative abundance of F. nucleatum and pks⁺ E. coli in fecal samples by quantitative PCR. Receiver operating characteristic curve (ROC) analyses were used to analyze the diagnostic value of single or combined biomarkers.

RESULTS

Fecal F. nucleatum and pks⁺ E. coli levels were higher in the CRC group in either the CAP group or healthy controls (P = 0.02; 0.01). There was no statistical difference in the distribution of F. nucleatum and pks⁺ E. coli in patients with different tumor sites (P > 0.05). The combination of F. nucleatum+pks⁺ E. coli+CEA+CA19-9+FOBT was chosen as the optimal panel in differentiating both CRC and CAP from the controls. The combination of F. nucleatum, pks⁺ E. coli, and FOBT improved diagnostic efficiency. However, there was difficulty in differentiating CRC from CAP.

CONCLUSION

Our results suggested that combining bacterial markers with conventional tumor markers improves the diagnostic efficiency for noninvasive diagnosis of CRC.

MicroRNA-26b-5p promotes development of neonatal respiratory distress syndrome by inhibiting differentiation of mesenchymal stem cells to type II of alveolar epithelial cells via regulating Wnt5a

OBJECTIVE

The aim was to investigate the role of microRNA-26b-5p in regulating mesenchymal stem cells (MSCs) differentiation to type II of alveolar epithelial cells (AECII) in the disease course of neonatal respiratory distress syndrome (NRDS).

MATERIALS AND METHODS

MSCs were first derived from rat bone marrow. In vitro induction of MSCs differentiation to AECII was conducted by SAGM. The mRNA levels of microRNA-26b-5p, Wnt5a, and AECII-related genes (Occludin, KGF, CK18, SpA, SpB, and SpC) during the process of cell differentiation were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). Enzyme-linked immunosorbent assay (ELISA) was conducted for detecting levels of inflammatory factors tumor necrosis factor-α (TNF-α), interferon-α (INF-α), and interleukin-1 (IL-1) in cell supernatant. Dual-luciferase reporter gene assay was then carried out to verify the regulatory effect of microRNA-26b-5p on Wnt5a. MicroRNA-26b-5p expression in serum samples of NRDS neonates and healthy neonates was detected by qRT-PCR as well.

RESULTS

MicroRNA-26b-5p was overexpressed in NRDS neonates than those of healthy neonates. Besides, microRNA-26b-5p was highly expressed in the process of MSCs differentiation to AECII. MicroRNA-26b-5p overexpression remarkably inhibited AECII differentiation and Wnt5a expression. Levels of TNF-α, INF-α, and IL-1 in cell supernatant during differentiation induction were elevated. The regulatory effects of microRNA-26b-5p on AECII differentiation, Wnt5a expression, and inflammatory response were reversed by Wnt5a overexpression.

CONCLUSIONS

MicroRNA-26b-5p inhibits MSCs differentiation to AECII via inhibiting Wnt5a expression through the Wnt pathway.

[Changes of retinal structure after systemic immunosuppressive treatment in eyes with Vogt-Koyanagi-Harada disease]

Objective: To assess structural changes in retina after systemic immunosuppressive treatment in Vogt-Koyanagi-Harada (VKH) disease using spectral-domain optical coherence tomography (SD-OCT). Methods: The clinical data of 17 VKH cases (34 eyes) who consecutively attended the Beijing Tongren Hospital between December 2015 and December 2019 were retrospectively reviewed. All the patients had acute or subacute onset, and underwent high-dose systemic corticosteroid and/or immunosuppressive treatment, with a followed-up time of at least 6 months. At the end of follow-up, the intraocular inflammation was controlled, and oral prednisone was withdrawn or being adjusted to less than 10 mg/day. The SD-OCT features of the included eyes were analyzed before treatment, 1 week, 1 month and 3 months after treatment, and at the last visit. Results: A total of 17 cases (34 eyes; 6 males and 11 females) were included, with an age of (42.2±10.6) years, and were followed up for (9.4±3.3) months. At 1 week after initiating treatment, the percentage of the eyes with extensive/multiple or multifocal retinal detachment in the macular region, membranous structures and intraretinal cysts, and undulations and bumps of retinal pigment epithelium (RPE) decreased (5.9% vs 100%, 2.9% vs 47.1%, 5.9% vs 70.6%, 11.8% vs 58.8%, respectively, all P<0.001). There was statistical significant difference of the percentage of ellipsoid zone and external limiting membrane (ELM) disruptions before treatment, at 3 months and the last visit (100% vs 35.3%, 64.7% vs 52.9%, 41.2% vs 26.5%, respectively, all P<0.001). At the last visit, there were statistical significant differences of the best corrected vision acuity (BCVA) between the intact ellipsoid zone group (20 eyes) and the discontinuous group (14 eyes), as well as between the intact ELM group (25 eyes) and the discontinuous group (9 eyes), respectively [0 (0, 0.05) vs 0.10 (0.03, 0.33) (log MAR), P=0.004; 0 (0, 0.07) vs 0.22 (0.05, 0.40) (log MAR), P=0.005]. Conclusions: The edema of choroid and retina subsided obviously at 1 week after initiating treatment. The extent of damage and recovery ability of ellipsoid zone and ELM were different before treatment, at 3 months and the last visit. At the last visit, the outer retinal layers failed to recover completely in some patients, and were related to the BCVA.

Microbiome in Intestinal Lavage Fluid May Be A Better Indicator in Evaluating The Risk of Developing Colorectal Cancer Compared with Fecal Samples

OBJECTIVE

Intestinal microbiota plays a vital role in the pathogenesis of colorectal cancer (CRC), which is crucial for assessing the risk and prognosis of CRC. Most studies regarding human gut microbiota mainly based on the feces, but the exact composition of microbiota vary significantly due to fecal composition is easily affected by many factors. We aim to evaluate whether intestinal lavage fluid (IVF) is a better substitution mirroring the gut microbiota.

METHODS

We performed 16S rRNA gene analysis on fecal and IVF samples from 30 CRC patients and 25 healthy individuals, comparison in luminal (feces) / mucosal (IVF) adherent bacterial community profiles were analyzed.

RESULTS

The difference between feces and IVF were observed, including the diversity and abundance of pathogenic bacteria (either in single strain or in co-occurrence pattern). IVF group shared 605 OTUs with the fecal group, but there was 94 OTUs only observed in fecal samples, while 247 OTUs were mainly existing in the IVF group. Among them, 27 vital bacterial species detected in IVF, while 10 critical species detected in fecal samples. The co-occurrence bacteria Fusobacteria Cluster and Proteobacteria Cluster 2 significantly increased in IVF than in control (P < .01), while Firmicutes Cluster 1, Firmicutes Cluster 2 and Proteobacteria Cluster 1 were markedly lower in IVF than in control (P < .001). In CRC feces, Fusobacteria Cluster was higher than in control (P < .05), but Firmicutes Cluster 1 was of substantially less abundance than in control (P < .001). Proteobacteria Cluster 2 was increased dramatically in IVF than in feces (P < .05), Firmicutes Cluster 1 were of substantially less abundance than in feces (P < .05).

CONCLUSION

Pathogenic microbiota is more abundant in IVF than in feces. Microbiota of IVF may closely be related to the mucosal-associated microbial communities, which benefit from elucidating the relationship of the intestinal microbiota and CRC carcinogenesis.

Selection of an Optimal Combination Panel to Better Triage COVID-19 Hospitalized Patients

PURPOSE

It is difficult to predict the prognosis of COVID-19 patients at the disease onset. This study was designed to add new biomarkers into conventional inflammatory panels to build an optimal combination panel, to better triage patients and predict their outcomes.

PATIENTS AND METHODS

Biochemical parameters representing multi-organ functions, cytokines, acute-phase proteins, and other inflammatory markers were measured in COVID-19 patients on hospital admission. Receiver operating characteristic (ROC) curves, logistic regression, event-free survival (EFS), and Cox analyses were performed to screen and compare the predictive capabilities of the new panel in patients with different illness severity and outcome.

RESULTS

This study included 120 patients with COVID-19, consisting of 32 critical, 28 severe, and 60 mild/moderate patients. Initial levels of the selected biomarkers showed a significant difference in the three groups, all of which influenced patient outcome and EFS to varying degrees. Cox proportional hazard model revealed that procalcitonin (PCT) and interleukin 10 (IL-10) were independent risk factors, while superoxide dismutase (SOD) was an independent protective factor influencing EFS. In discriminating the critical and mild patients, a panel combining PCT, IL-6, and neutrophil (NEUT) yielded the best diagnostic performance with an AUC of 0.99, the sensitivity of 90.60% and specificity of 100%. In distinguishing between severe and mild patients, SOD's AUC of 0.89 was higher than any other single biomarker. In differentiating the critical and severe patients, the combination of white blood cell count (WBC), PCT, IL-6, IL-10, and SOD achieved the highest AUC of 0.95 with a sensitivity of 75.00% and specificity of 100%.

CONCLUSION

The optimal combination panel has a substantial potential to better triage COVID-19 patients on admission. Better triage of patients will benefit the rational use of medical resources.

Cellular Retinoic-Acid Binding Protein 2 in Solid Tumor

The retinoic acid (RA) signaling pathway is crucial for many biological processes. The RA transporter, Cellular Retinoic-Acid Binding Protein 2 (CRABP2), is abnormally expressed in various tumor types. CRABP2 presents significant effects on tumorous behaviors and functions, including cell proliferation, apoptosis, invasion, migration, metastasis, and angiogenesis. The tumorigenesis mechanism of CRABP2, as both suppressor and promotor, is complicated, therefore, there remains the need for further investigation. Elucidating the regulating mechanisms in a specific stage of the tumor could facilitate CRABP2 to be a biomarker in cancer diagnosis and prognosis. Besides, clarifying the pathways of CRABP2 in cancer development will contribute to the gene-targeted therapy. In this review, we summarized the expression, distribution, and mechanism of CRABP2 in solid tumors. Illuminating the CRABP2 signaling pathway may benefit understanding the retinoid signaling pathway, providing a useful biomarker for future clinical trials.

Gene Expression Analysis of Human Papillomavirus-Associated Colorectal Carcinoma

PURPOSE

Human papillomavirus (HPV) antigens had been found in colorectal cancer (CRC) tissue, but little evidence demonstrates the association of HPV with oncogene mutations in CRC. We aim to elucidate the mutated genes that link HPV infection and CRC carcinogenesis.

METHODS

Cancerous and adjacent noncancerous tissues were obtained from CRC patients. HPV antigen was measured by using the immunohistochemical (IHC) technique. The differentially expressed genes (DEGs) in HPV-positive and HPV-negative tumor tissues were measured by using TaqMan Array Plates. The target genes were validated with the qPCR method.

RESULTS

15 (31.9%) cases of CRC patients were observed to be HPV positive, in which HPV antigen was expressed in most tumor tissues rather than in adjacent noncancerous tissues. With TaqMan Array Plates analyses, we found that 39 differentially expressed genes (DEGs) were upregulated, while 17 DEGs were downregulated in HPV-positive CRC tissues compared with HPV-negative tissues. Four DEGs (MMP-7, MYC, WNT-5A, and AXIN2) were upregulated in tumor vs. normal tissues, or adenoma vs. normal tissue in TCGA, which was overlapped with our data. In the confirmation test, MMP-7, MYC, WNT-5A, and AXIN2 were upregulated in cancerous tissue compared with adjacent noncancerous tissue. MYC, WNT-5A, and AXIN2 were shown to be upregulated in HPV-positive CRC tissues when compared to HPV-negative tissues.

CONCLUSION

HPV-encoding genome may integrate into the tumor genomes that involved in multiple signaling pathways. Further genomic and proteomic investigation is necessary for obtaining a more comprehensive knowledge of signaling pathways associated with the CRC carcinogenesis.

The accuracy of bone mineral density measurement using dual-energy spectral CT and quantitative CT: a comparative phantom study

AIM

To compare bone mineral density (BMD) measurement accuracy by dual-energy spectral computed tomography (CT) and quantitative CT (QCT) using an anthropomorphic European spine phantom (ESP).

MATERIALS AND METHODS

An ESP containing three hydroxyapatite inserts with densities of 50, 100, and 200 mg/cm³ was scanned 10 times each using spectral CT and QCT protocols. Their BMD values were measured using hydroxyapatite-based spectral CT material decomposition images and QCT images and compared with the true values in ESP.

RESULTS

Both protocols had good repeatability in BMD measurement with low coefficient-of-variance (spectral CT: <2.31%; QCT: <1.17%). There were biases in BMD measurement for the 50, 100, and 200 mg/cm³ hydroxyapatite insert with relative errors of 2.34% (48.83±1.13 mg/cm³), 2% (98±1.25 mg/cm³) and 5.96% (188.09±2.11 mg/cm³), in spectral CT, and 11% (55.5±0.65 mg/cm³), 9.85% (109.85±0.42 mg/cm³) and 4.04% (208.07±0.54 mg/cm³) in QCT, respectively.

CONCLUSION

BMD can be accurately measured using either QCT or spectral CT, and spectral CT has smaller bias than QCT.

Molecular cloning and functional characterisation of duck (Anas platyrhynchos) tumour necrosis factor receptor-associated factor 3

1. Tumour necrosis factor receptor-associated factor 3 (TRAF3) is a key regulator of innate immunity and acquired immunity, and has a salient anti-viral role. 2. In this experiment, the duck TRAF3 (DuTRAF3) gene was cloned according to the Anas platyrhynchos TRAF3 sequence to explore its function. The TRAF3 open reading frame contains 1704 bp that encode a protein of 567 amino acids, which contain a RING finger domain, two zinc finger motifs, a coiled-coil region, and a MATH domain. 3. Reverse transcription-polymerase chain reaction showed that DuTRAF3 was expressed in all the examined tissues, with a comparatively higher expression in the spleen and brain tissues. 4. In HEK293T cells, DuTRAF3 overexpression resulted in a significantly increased NF-κB activity and interferon (IFN)-β promoter activation. 5. Following resiquimod (R848) and poly(I:C) stimulation of duck peripheral blood mononuclear cells (PBMCs), the expressions of TRAF3 and IFN-β were significantly upregulated; in addition, following R848 stimulation, the mRNA levels of IL-6, IL-8 and IL-10 were also significantly upregulated. After infection with the Newcastle Disease Virus LaSota vaccine strain, the mRNA levels of IL-6 and IL-10 were significantly upregulated, while that of TRAF3 was downregulated. 6. These results suggest that DuTRAF3 has an important role to play in innate antiviral immune responses.

Gradient magnet design for simultaneous detection of electrons and positrons in the intermediate MeV range

We report the design and development of a compact electron and positron spectrometer based on tapered neodymium iron boron magnets to characterize the pairs generated in laser-matter experiments. The tapered design forms a gradient magnetic field component allowing energy dependent focusing of the dispersed charged particles along a chosen detector plane. The mirror symmetric design allows for simultaneous detection of pairs with energies from 2 MeV to 500 MeV with an accuracy of ≤10% in the wide energy range from 5 to 110 MeV for a parallel beam incident on a circular aperture of 20 mm. The energy resolution drops to ≤20% for 4-90 MeV range for a divergent beam originating from a point source at 20 cm away (i.e., a solid angle of ∼8 milli steradians), with ≤10% accuracy still maintained in the narrower energy range from 10 to 55 MeV. It offers higher solid angle acceptance, even for the divergent beam, compared to the conventional pinhole aperture-based spectrometers. The proposed gradient magnet is suitable for the detection of low flux and/or monoenergetic type electron/positron beams with finite transverse sizes and offers unparalleled advantages for gamma-ray spectroscopy in the intermediate MeV range.